Based on what both Matthew Vaughn and Bryan Singer has said this film could be set In 1960's.Vaughn has mentioned wanting the film to beguin with Magneto responable
for JFK's assassination.This could set up a film with Magneto and Brotherhood beguin terrorist attacks aginst US Government with the Civil Right movement or vietnam war
protests as backdrop.

You can have Logan as CIA or Special Military ops sent after Magneto who ends up crossing paths with the first X-Men team.He would be preadamanutum.Vaughn and Singer have already shown they have no concern with Ignoring The Last Stand.That would be applied because Beast has no memory of Wolverine before their meeting In The Last Stand.

Cyclops,STorm,and Jean Grey will not be In this film.Now If you say X-Men and X2 take place In 1990's.In a 1970's set third film you could get away with teenage
versions of them showing up.

People are wanting too many new characters to show up.You have a great opportunity for a X-Men VS Brotherhood film.The third film should be when a new enemy causes them to work together.It would be Ideal to have Sinster as Villain for third film when they Introduce Teenage Cyclops.

Logan could be major supporting character In this film.And having him In film could fit with X-Men and X2.